TY  - JOUR
A1  - Shityakov, Sergey
A1  - Dandekar, Thomas
T1  - Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function
N2  - Indinavir (Crivaxan®) is a potent inhibitor of the HIV (human immunodeficiency virus) protease. This enzyme has an important role in viral replication and is considered to be very attractive target for new antiretroviral drugs. However, it becomes less effective due to highly resistant new viral strains of HIV, which have multiple mutations in their proteases. For this reason, we used a lead expansion method to create a new set of compounds with a new mode of action to protease binding site. 1300 compounds chemically diverse from the initial hit were generated and screened to determine their ability to interact with protease and establish their QSAR properties. Further computational analyses revealed one unique compound with different protease binding ability from the initial hit and its role for possible new class of protease inhibitors is discussed in this report.
KW  - Proteasen
KW  - protease; Indinavir; lead expansion; docking; pharmacophore
Y1  - 2010
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-67824
ER  - 
TY  - THES
A1  - Shityakov, Sergey
T1  - Molecular modelling and simulation of retroviral proteins and nanobiocomposites
T1  - Simulationen und Interaktionen viraler Proteine sowie von   Kohlenstoffenanoröhren mit Membranen und Proteinen
N2  - Molecular modelling and simulation are powerful methods in providing important in-formation on different biological systems to elucidate their structural and functional proper-ties, which cannot be determined in experiment. These methods are applied to analyse versa-tile biological systems: lipid membrane bilayers stabilized by an intercalated single wall carbon nanotube and retroviral proteins such as HIV protease and integrase. HIV-1 integrase has nuclear localization signals (NLS) which play a crucial role in nuclear import of viral preintegration complex (PIC). However, the detailed mechanisms of PIC formation and its nuclear transport are not known. Previously it was shown that NLSs bind to the cell transport machinery e.g. proteins of nuclear pore complex such as transportins. I investigated the interaction of this viral protein HIV-1 integrase with proteins of the nuclear pore complex such as transportin-SR2 (Shityakov et al., 2010). I showed that the transportin-SR2 in nuclear import is required due to its interaction with the HIV-1 integrase. I analyzed key domain interaction, and hydrogen bond formation in transportin-SR2. These results were discussed in comparison to other retroviral species such as foamy viruses to better understand this specific and efficient retroviral trafficking route. The retroviral nuclear import was next analyzed in experiments regarding the retroviral ability to infect nondividing cells. To accomplish the gene transfer task successfully, ret-roviruses must efficiently transduce different cell cultures at different phases of cell cycle. However, promising and safe foamy viral vectors used for gene transfer are unable to effi-ciently infect quiescent cells. This drawback was due to their inability to create a preintegra-tion complex (PIC) for nuclear import of retroviral DNA. On the contrary, the lentiviral vec-tors are not dependant on cell cycle. In the course of reverse transcription the polypurine tract (PPT) is believed to be crucial for PIC formation. In this thesis, I compared the transduction frequencies of PPT modified FV vectors with lentiviral vectors in nondividing and dividing alveolar basal epithelial cells from human adenocarcinoma (A549) by using molecular cloning, transfection and transduction techniques and several other methods. In contrast to lentiviral vectors, FV vectors were not able to effi-ciently transduce nondividing cell (Shityakov and Rethwilm, unpublished data). Despite the findings, which support the use of FV vectors as a safe and efficient alternative to lentiviral vectors, major limitation in terms of foamy-based retroviral vector gene transfer in quiescent cells still remains. Many attempts have been made recently to search for the potential molecules as pos-sible drug candidates to treat HIV infection for over decades now. These molecules can be retrieved from chemical libraries or can be designed on a computer screen and then synthe-sized in a laboratory. Most notably, one could use the computerized structure as a reference to determine the types of molecules that might block the enzyme. Such structure-based drug design strategies have the potential to save off years and millions of dollars compared to a more traditional trial-and-error drug development process. After the crystal structure of the HIV-encoded protease enzyme had been elucidated, computer-aided drug design played a pivotal role in the development of new compounds that inhibit this enzyme which is responsible for HIV maturation and infectivity. Promising repre-sentatives of these compounds have recently found their way to patients. Protease inhibitors show a powerful sustained suppression of HIV-1 replication, especially when used in combi-nation therapy regimens. However, these drugs are becoming less effective to more resistant HIV strains due to multiple mutations in the retroviral proteases. In computational drug design I used molecular modelling methods such as lead ex-pansion algorithm (Tripos®) to create a virtual library of compounds with different binding affinities to protease binding site. In addition, I heavily applied computer assisted combinato-rial chemistry approaches to design and optimize virtual libraries of protease inhibitors and performed in silico screening and pharmacophore-similarity scoring of these drug candidates. Further computational analyses revealed one unique compound with different protease bind-ing ability from the initial hit and its role for possible new class of protease inhibitors is dis-cussed (Shityakov and Dandekar, 2009). A number of atomistic models were developed to elucidate the nanotube behaviour in lipid bilayers. However, none of them provided useful information for CNT effect upon the lipid membrane bilayer for implementing all-atom models that will allow us to calculate the deviations of lipid molecules from CNT with atomistic precision. Unfortunately, the direct experimental investigation of nanotube behaviour in lipid bilayer remains quite a tricky prob-lem opening the door before the molecular simulation techniques. In this regard, more de-tailed multi-scale simulations are needed to clearly understand the stabilization characteristics of CNTs in hydrophobic environment. The phenomenon of an intercalated single-wall carbon nanotube in the center of lipid membrane was extensively studied and analyzed. The root mean square deviation and root mean square fluctuation functions were calculated in order to measure stability of lipid mem-branes. The results indicated that an intercalated carbon nanotube restrains the conformational freedom of adjacent lipids and hence has an impact on the membrane stabilization dynamics (Shityakov and Dandekar, 2011). On the other hand, different lipid membranes may have dissimilarities due to the differing abilities to create a bridge formation between the adherent lipid molecules. The results derived from this thesis will help to develop stable nanobiocom-posites for construction of novel biomaterials and delivery of various biomolecules for medi-cine and biology.
N2  - Molekulare Modellierung und Simulationen sind leistungsstarke Methoden, um wich-tige Informationen von verschiedenen biologischen Systemen, welche nicht durch Experi-mente erschlossen werden können, darzustellen, und deren strukturelle und funktionelle Ei-genschaften aufzuklären. Diese Arbeit untersucht in Simulationen Interaktionen viraler Proteinen sowie von Kohlenstoffenanoröhren mit Membranen und Proteinen. Die HIV-1 Integrase besitzt Kernlokalisierungssignale („nuclear localization signals [NLS]“), welche eine entscheidende Rolle beim Import des viralen Präintegrationskomplexes („preintegration complex [PIC]“) in den Zellkern spielen. Die Ausbildung des PIC und sein Import in den Zellkern sind im Detail noch nicht bekannt. Es wurde bereits gezeigt, dass die NLS an Moleküle des Zelltransportsystems binden, wie z.B. an Transportinkernporen. Im Rahmen meiner Arbeit untersuchte ich die Interaktionen der viralen HIV-1 Integrase mit Proteinen der Kernporen wie dem Transportin-SR2 Protein (Shityakov et al., 2010). Hierbei wurden die möglichen Interaktionen des Transportin-SR2 Protein mit der HIV-1-Integrase und die Bedeutung dieser Interaktionen mit dem Import in den Kern aufgezeigt. Zudem wur-den die Interaktionen der Schlüsseldomänen und die Ausbildung von Wasserstoffbrücken-bindungen im dem Transportin-SR2 Protein untersucht. Die Ergebnisse wurden mit Protein-komplexen andere retroviralen Spezies, wie z.B. dem humanen Spumaretrovirus („human foamy virus [HFV]“), verglichen, um diesen spezifischen und sehr effizienten retroviralen Transportweg in die Wirtszelle zu entschlüsseln. Der experimentelle Teil dieser Arbeit beschäftigte sich damit, den retroviralen Kern-import zu untersuchen, um die Fähigkeit des Retrovirus, nicht teilende Zellen zu infizieren, besser zu verstehen verstanden wird. Um dies zu bewerkstelligen, müssen Retroviren Zellkul-turen in verschiedenen Stadien des Zellzyklus effizient transduzieren. Vielversprechende und sichere- HFV- Vektoren, welche in der Gentherapie eingesetzt werden könnten, sind nicht in der Lage, diese Effizienz bei ruhenden Zellen zu gewährleisten. Dies rührte daher, dass diese nicht in der Lage waren, einen PIC für den Transport der retroviralen DNA auszubilden. Lentivirale Vektoren sind dagegen nicht auf einen bestimmten Zellzyklus angewiesen. Für die reverse Transkription ist der Polypurinteil („polypurine tract [PPT]“) essentiell für die Ausbildung der PIC. In dieser Doktorarbeit vergleiche ich die Transduktionsfrequenz von PPT-modifizierten HFV-Vektoren mit denen von lentiviralen Vektoren in nichtteilenden und tei-lenden Lungenkarzinomepithelzellen. Hierbei wurden Methoden wie Klonierung, Transfektion, und Transduktion (wie auch weitere Methoden) angewendet. Im Gegensatz zu lentiviralen Vektoren konnten HFV-Vektoren sich nicht teilende Zellen in meinen Versuchen nicht effizient transduzieren (Shityakov und Rethwiln, unveröffentlicht). Trotz der Befunde, dass HFV-Vektoren sichere und effiziente Alternativen zu lentiviralen Vektoren darstellen, bestehen immer noch große Einschränkungen, diese HFV-basierten, retroviralen Vektoren für Gentherapien bei ruhenden Zellen einzusetzen. Viele Versuche wurden unternommen, um mögliche, vielversprechende Moleküle, welche als Wirkstoffe für eine HIV-Therapie eingesetzt werden könnten, zu finden. Diese Moleküle können aus chemischen Substanzbibliotheken bezogen werden oder am Computer in silico entworfen und dann synthetisiert werden. Digitalisierte Strukturen können als Refe-renzen benutzt werden, um besser herauszufinden, wie diese Moleküle Typen diverse Enzy-me blokieren könnten. Strukturbasiertes Wirkstoffdesign hat das Potential, viele Jahre und Geld an Entwicklungskosten einzusparen. Nachdem die Kristallstruktur der HIV-kodierten Proteasen aufgeklärt war, spielte das computergestützte Wirkstoffdesign eine zentrale Rolle bei der Entwicklung neuer Wirkstoffe gegen die Protease. Vielversprechende Vertreter dieser Wirkstoffklasse werden seit kurzem nun auch für die Behandlung von Patienten eingesetzt. Proteaseinhibitoren zeigen eine wir-kungsvolle und langanhaltende Inhibition der HIV-1-Replikation; besonders dann, wenn sie in Kombinationstherapien eingesetzt werden. Aber diese Wirkstoffe werden immer weniger effektiv, je resistenter die HIV-Stämme durch Mutationen in den retroviralen Proteasen wer-den. Im Rahmen meiner Arbeit mit computergestütztem Wirkstoffdesign nutzte ich Model-lierungsmethoden wie den „lead expansion algorithm“ (Tripos®) um virtuelle Wirkstoffbibli-otheken mit verschiedenen Affinitäten zur Proteasebindungsstelle zu erstellen. Zusätzlich wandte ich Verfahren der computergestützten, kombinatorischen Chemie an, um virtuelle Bibliotheken von Proteaseinhibitoren zu designen, und zu verbessern. Parallel dazu wurde eine in silico Selektion sowie eine Einteilung nach Pharmakophorähnlichkeiten für diese Kandidaten vorgenommen. Weiterführende computergestützte Analysen förderten einen ein-zigartigen Wirkstoff zu Tage, welcher neuartige Proteasebindungseigenschaften aufweist, und dessen Rolle für eine potentiell neuartige Klasse von Proteaseinhibitoren schon beschrieben wurde (Shityakov und Dandekar, 2009). Eine Reihe von Modellen mit atomarer Auflösung wurden bereits entwickelt, um das Verhalten von Nanoröhren in Lipid-Doppelschichten aufzuklären. Die Auswirkungen auf die molekular Dynamik einer einschichtigen Karbonnanoröhre, welche in das Zentrum einer Lipid-Doppelschicht eingefügt wurde, wurden intensiv studiert und analysiert. Die Normalabweichung und Fluktuationen wurden berechnet, um eine Aussage über die Stabilität der Lipid-Doppelschichten treffen zu können. Die Ergebnisse weisen darauf hin, dass eine eingefügte Karbonnanoröhre die Freiheit für Konformationsänderungen bei nahegelegenen Lipiden einschränkt und dadurch einen Einfluss auf die Membranstabilität hat (Shityakov und Dandekar, 2011). Es kann aber außer-dem sein, dass verschiedene Lipid-Doppelschichten Unterschiede in ihrer Fähigkeit, Brücken zwischen benachbarten Lipiden auszubilden, aufweisen. Viren und Karbonnanoröhren werden damit in verschiedenen dynamischen Simulati-onen untersucht, um mehr über ihre Interaktionen mit Proteinen und Membranen zu erfahren.
KW  - Kohlenstoff
KW  - Nanoröhre
KW  - Retroviren
KW  - Proteine
KW  - virale Proteine
KW  - retroviral proteins
KW  - nanobiocomposites
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-56960
ER  - 
TY  - JOUR
A1  - Shityakov, Sergey
A1  - Broscheit, Jens
A1  - Förster, Carola
T1  - Multidrug resistance protein P-gp interaction with nanoparticles (fullerenes and carbon nanotube) to assess their drug delivery potential: a theoretical molecular docking study.
JF  - International journal of computational biology and drug design
N2  - P-glycoprotein (P-gp)-mediated efflux system plays an important role to maintain chemical balance in mammalian cells for endogenous and exogenous chemical compounds. However, despite the extensive characterisation of P-gp potential interaction with drug-like molecules, the interaction of carbon nanoparticles with this type of protein molecule is poorly understood. Thus, carbon nanoparticles were analysed, such as buckminsterfullerenes (C20, C60, C70), capped armchair single-walled carbon nanotube (SWCNT or C168), and P-gp interactions using different molecular docking techniques, such as gradient optimisation algorithm (ADVina), Lamarckian genetic algorithm (FastDock), and shape-based approach (PatchDock) to estimate the binding affinities between these structures. The theoretical results represented in this work show that fullerenes might be P-gp binders because of low levels of Gibbs free energy of binding (ΔG) and potential of mean force (PMF) values. Furthermore, the SWCNT binding is energetically unfavourable, leading to a total decrease in binding affinity by elevation of the residual area (Ares), which also affects the π-π stacking mechanisms. Further, the obtained data could potentially call experimental studies using carbon nanostructures, such as SWCNT for development of drug delivery vehicles, to administer and assess drug-like chemical compounds to the target cells since organisms probably did not develop molecular sensing elements to detect these types of carbon molecules.
KW  - SWCNT CNTs
KW  - pi-pi stacking
KW  - mean force potential
KW  - Gibbs free energy of binding
KW  - molecular docking
KW  - shape-based approach
KW  - Lamarckian genetic algorithms
KW  - gradient optimisation
KW  - drug delivery
KW  - multidrug resistance
KW  - P-glycoprotein
KW  - carbon nanoparticles
KW  - fullerenes
KW  - single-walled carbon nanotubes
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-132089
VL  - 6
IS  - 4
ER  - 
TY  - JOUR
A1  - Salvador, Ellaine
A1  - Shityakov, Sergey
A1  - Förster, Carola
T1  - Glucocorticoids and endothelial cell barrier function
JF  - Cell and Tissue Research
N2  - Glucocorticoids (GCs) are steroid hormones that have inflammatory and immunosuppressive effects on a wide variety of cells. They are used as therapy for inflammatory disease and as a common agent against edema. The blood brain barrier (BBB), comprising microvascular endothelial cells, serves as a permeability screen between the blood and the brain. As such, it maintains homeostasis of the central nervous system (CNS). In many CNS disorders, BBB integrity is compromised. GC treatment has been demonstrated to improve the tightness of the BBB. The responses and effects of GCs are mediated by the ubiquitous GC receptor (GR). Ligand-bound GR recognizes and binds to the GC response element located within the promoter region of target genes. Transactivation of certain target genes leads to improved barrier properties of endothelial cells. In this review, we deal with the role of GCs in endothelial cell barrier function. First, we describe the mechanisms of GC action at the molecular level. Next, we discuss the regulation of the BBB by GCs, with emphasis on genes targeted by GCs such as occludin, claudins and VE-cadherin. Finally, we present currently available GC therapeutic strategies and their limitations.
KW  - endothelial cells
KW  - glucocorticoids
KW  - glucocorticoid receptor
KW  - blood brain barrier
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-132091
VL  - 355
IS  - 3
ER  - 
TY  - JOUR
A1  - Shityakov, Sergey
A1  - Förster, Carola
T1  - Pharmacokinetic Delivery and Metabolizing Rate of Nicardipine Incorporated in Hydrophilic and Hydrophobic Cyclodextrins Using Two-Compartment Mathematical Model
JF  - The Scientific World Journal
N2  - The dispersion routes of cyclodextrin complexes with nicardipine (NC), such as hydrophilic hydroxypropyl-\(\beta\)-cyclodextrin (NC/HP\(\beta\)CD) and hydrophobic triacetyl-\(\beta\)-cyclodextrin (NC/TA\(\beta\)CD), through the body for controlled drug delivery and sustained release have been examined. The two-compartment pharmacokinetic model described the mechanisms of how the human body handles with ingestion of NC-cyclodextrin complexes in gastrointestinal tract (GI), distribution in plasma, and their metabolism in the liver. The model showed that drug bioavailability was significantly improved after oral administration of cyclodextrin complexes. The mathematical significance of this study to predict nicardipine delivery using pharmacokinetic two-compartment mathematical model with linear ordinary differential equations (ODE) approach represents a valuable tool to emphasize its effectiveness and metabolizing rate and diminish the side effects.
KW  - pharmacokinetic delivery
KW  - metabolizing rate
KW  - Nicardipine
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-130519
VL  - 2013
IS  - 131358
ER  - 
TY  - JOUR
A1  - Shityakov, Sergey
A1  - Sohajda, Tamás
A1  - Puskas, Istaván
A1  - Roewer, Norbert
A1  - Förster, Carola
A1  - Broscheit, Jens-Albert
T1  - Ionization States, Cellular Toxicity and Molecular Modeling Studies of Midazolam Complexed with Trimethyl-β-Cyclodextrin
JF  - Molecules
N2  - We investigated the ionization profiles for open-ring (OR) and closed-ring (CR) forms of midazolam and drug-binding modes with heptakis-(2,3,6-tri-O-methyl)-β-cyclodextrin (trimethyl-β-cyclodextrin; TRIMEB) using molecular modeling techniques and quantum mechanics methods. The results indicated that the total net charges for different molecular forms of midazolam tend to be cationic for OR and neutral for CR at physiological pH levels. The thermodynamic calculations demonstrated that CR is less water-soluble than OR, mainly due to the maximal solvation energy (ΔG(CR)(solv = -9.98 kcal·mol ⁻¹), which has a minimal ΔG(OR)(solv) of -67.01 kcal·mol⁻¹. A cell viability assay did not detect any signs of TRIMEB and OR/CR-TRIMEB complex toxicity on the cEND cells after 24 h of incubation in either Dulbecco's Modified Eagles Medium or in heat-inactivated human serum. The molecular docking studies identified the more flexible OR form of midazolam as being a better binder to TRIMEB with the fluorophenyl ring introduced inside the amphiphilic cavity of the host molecule. The OR binding affinity was confirmed by a minimal Gibbs free energy of binding (ΔG(bind)) value of -5.57 ± 0.02 kcal·mol⁻¹, an equilibrium binding constant (K(b)) of 79.89 ± 2.706 μM, and a ligand efficiency index (LE(lig)) of -0.21 ± 0.001. Our current data suggest that in order to improve the clinical applications of midazolam via its complexation with trimethyl-β-cyclodextrin to increase drug's overall aqueous solubility, it is important to concern the different forms and ionization states of this anesthetic. All mean values are indicated with their standard deviations.
KW  - quantum mechanics
KW  - free energy of solvation
KW  - torsional energy
KW  - trimethyl-β-cyclodextrin
KW  - midazolam
KW  - transition state
KW  - molecular docking
KW  - Gibbs free energy of binding
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-119186
VL  - 19
IS  - 10
ER  - 
TY  - JOUR
A1  - Shityakov, Sergey
A1  - Förster, Carola
T1  - In silico predictive model to determine vector-mediated transport properties for the blood-brain barrier choline transporter
JF  - Advances and Applications in Bioinformatics and Chemistry
N2  - The blood–brain barrier choline transporter (BBB-ChT) may have utility as a drug delivery vector to the central nervous system (CNS). We therefore initiated molecular docking studies with the AutoDock and AutoDock Vina (ADVina) algorithms to develop predictive models for compound screening and to identify structural features important for binding to this transporter. The binding energy predictions were highly correlated with r2=0.88, F=692.4, standard error of estimate =0.775, and P-value<0.0001 for selected BBB-ChT-active/inactive compounds (n=93). Both programs were able to cluster active (Gibbs free energy of binding <−6.0 kcal*mol-1) and inactive (Gibbs free energy of binding >−6.0 kcal*mol-1) molecules and dock them significantly better than at random with an area under the curve value of 0.86 and 0.84, respectively. In ranking smaller molecules with few torsional bonds, a size-related bias in scoring producing false-negative outcomes was detected. Finally, important blood–brain barrier parameters, such as the logBBpassive and logBBactive values, were assessed to predict compound transport to the CNS accurately. Knowledge gained from this study is useful to better understand the binding requirements in BBB-ChT, and until such time as its crystal structure becomes available, it may have significant utility in developing a highly predictive model for the rational design of drug-like compounds targeted to the brain.
KW  - virtual screening
KW  - Gibbs free energy of binding
KW  - diffusion
KW  - molecular docking
KW  - drug delivery vector
KW  - central nervous system
KW  - blood–brain barrier choline transporter
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120200
VL  - 7
ER  - 
TY  - JOUR
A1  - Shityakov, Sergey
A1  - Förster, Carola
T1  - In silico structure-based screening of versatile P-glycoprotein inhibitors using polynomial empirical scoring functions
JF  - Advances and Applications in Bioinformatics and Chemistry
N2  - P-glycoprotein (P-gp) is an ATP (adenosine triphosphate)-binding cassette transporter that causes multidrug resistance of various chemotherapeutic substances by active efflux from mammalian cells. P-gp plays a pivotal role in limiting drug absorption and distribution in different organs, including the intestines and brain. Thus, the prediction of P-gp–drug interactions is of vital importance in assessing drug pharmacokinetic and pharmacodynamic properties. To find the strongest P-gp blockers, we performed an in silico structure-based screening of P-gp inhibitor library (1,300 molecules) by the gradient optimization method, using polynomial empirical scoring (POLSCORE) functions. We report a strong correlation (r2=0.80, F=16.27, n=6, P<0.0157) of inhibition constants (Kiexp or pKiexp; experimental Ki or negative decimal logarithm of Kiexp) converted from experimental IC50 (half maximal inhibitory concentration) values with POLSCORE-predicted constants (KiPOLSCORE or pKiPOLSCORE), using a linear regression fitting technique. The hydrophobic interactions between P-gp and selected drug substances were detected as the main forces responsible for the inhibition effect. The results showed that this scoring technique might be useful in the virtual screening and filtering of databases of drug-like compounds at the early stage of drug development processes.
KW  - multidrug resistance
KW  - molecular docking
KW  - POLSCORE
KW  - P-gp inhibitors
KW  - ATP-binding cassette transporter
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120214
VL  - 7
ER  - 
TY  - JOUR
A1  - Shityakov, Sergey
A1  - Puskás, István
A1  - Roewer, Norbert
A1  - Förster, Carola
A1  - Broscheit, Jens
T1  - Three-dimensional quantitative structure-activity relationship and docking studies in a series of anthocyanin derivatives as cytochrome P450 3A4 inhibitors
JF  - Advances and Applications in Bioinformatics and Chemistry
N2  - The cytochrome P450 (CYP)3A4 enzyme affects the metabolism of most drug-like substances, and its inhibition may influence drug safety. Modulation of CYP3A4 by flavonoids, such as anthocyanins, has been shown to inhibit the mutagenic activity of mammalian cells. Considering the previous investigations addressing CYP3A4 inhibition by these substances, we studied the three-dimensional quantitative structure-activity relationship (3D-QSAR) in a series of anthocyanin derivatives as CYP3A4 inhibitors. For the training dataset (n=12), comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) yielded crossvalidated and non-crossvalidated models with a q (2) of 0.795 (0.687) and r (2) of 0.962 (0.948), respectively. The models were also validated by an external test set of four compounds with r (2) of 0.821 (CoMFA) and r (2) of 0.812 (CoMSIA). The binding affinity modes associated with experimentally derived IC50 (half maximal inhibitory concentration) values were confirmed by molecular docking into the CYP3A4 active site with r (2) of 0.66. The results obtained from this study are useful for a better understanding of the effects of anthocyanin derivatives on inhibition of carcinogen activation and cellular DNA damage.
KW  - molecular docking
KW  - three-dimensional quantitative structure–activity relationship
KW  - cytochrome P450 3A4
KW  - comparative molecular similarity index analysis
KW  - comparative molecular field analysis
KW  - carcinogen activation
KW  - anthocyanin derivatives
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120226
VL  - 7
ER  - 
TY  - JOUR
A1  - Shityakov, Sergey
A1  - Förster, Carola
A1  - Rethwilm, Axel
A1  - Dandekar, Thomas
T1  - Evaluation and Prediction of the HIV-1 Central Polypurine Tract Influence on Foamy Viral Vectors to Transduce Dividing and Growth-Arrested Cells
N2  - Retroviral vectors are potent tools for gene delivery and various biomedical applications. To accomplish a gene transfer task successfully, retroviral vectors must effectively transduce diverse cell cultures at different phases of a cell cycle. However, very promising retroviral vectors based on the foamy viral (FV) backbone lack the capacity to efficiently transduce quiescent cells. It is hypothesized that this phenomenon might be explained as the inability of foamy viruses to form a pre-integration complex (PIC) with nuclear import activity in growth-arrested cells, which is the characteristic for lentiviruses (HIV-1). In this process, the HIV-1 central polypurine tract (cPPT) serves as a primer for plus-strand synthesis to produce a “flap” element and is believed to be crucial for the subsequent double-stranded cDNA formation of all retroviral RNA genomes. In this study, the effects of the lentiviral cPPT element on the FV transduction potential in dividing and growth-arrested (G1/S phase) adenocarcinomic human alveolar basal epithelial (A549) cells are investigated by experimental and theoretical methods. The results indicated that the HIV-1 cPPT element in a foamy viral vector background will lead to a significant reduction of the FV transduction and viral titre in growth-arrested cells due to the absence of PICs with nuclear import activity.
KW  - Evaluation
KW  - Prognose
KW  - HIV
KW  - Spumaviren
KW  - Einfluss
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-112763
ER  -